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STAT115 2020

STAT115 2020

Xiaole Shirley Liu via YouTube Direct link

STAT115 Chapter 5.2 Differential RNA-seq

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STAT115 Chapter 5.2 Differential RNA-seq

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STAT115 2020

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  1. 1 2020 STAT115 Lect1.1 Bioinfo History
  2. 2 2020 STAT115 Lect1.2 Big Data Challenge
  3. 3 2020 STAT115 Lect1.3 Bioinfo vs Comp Bio
  4. 4 2020 STAT115 Lect1.4 Course Info
  5. 5 STAT115 Chapter 3.1 Three Generations of Sequencing
  6. 6 STAT115 Chapter 3.2 FASTQ and FASTQC
  7. 7 STAT115 Chapter 3.4 BLAST and Suffix Arrays
  8. 8 STAT115 Chapter 3.5.1 BWT and LF Mapping
  9. 9 STAT115 Chapter 3.5.2 Borrows-Wheeler Alignment
  10. 10 STAT115 Chapter 3.6 SAM and BAM files
  11. 11 2020 STAT115 Lect3.1 RNA-seq Experimental Design
  12. 12 2020 STAT115 Lect3.2 RNA-seq Alignment and QC
  13. 13 2020 STAT115 Lect3.3 RNA-seq Quantification
  14. 14 2020 STAT115 Lect3.4 RNA-seq Read Distribution
  15. 15 STAT115 Chapter 5.2 Differential RNA-seq
  16. 16 STAT115 Chapter 5.3 Multiple Hypotheses Testing and False Discovery Rate
  17. 17 STAT115 Chapter 5.5 Gene Ontology
  18. 18 STAT115 Chapter 5.6 Gene Set Enrichment Analyses
  19. 19 STAT115 Chapter 6.1/2 Hierarchical Clustering
  20. 20 STAT115 Chapter 6.3 K-means Clustering
  21. 21 STAT115 Chapter 6.4 Considerations of Kmeans Clustering
  22. 22 2020 STAT115 Lect6.1 KNN and MDS
  23. 23 2020 STAT115 Lect6.2 PCA
  24. 24 STAT115 Chapter 6.5 Batch Effect Removal
  25. 25 2020 STAT115 Lect8.1 scRNA-seq
  26. 26 2020 STAT115 Lect8.2 Processing and QC scRNA-seq
  27. 27 2020 STAT115 Lect8.3 scRNA-seq Clustering and Visualization
  28. 28 2020 STAT115 Lect8.4 Differential Expression in scRNA-seq
  29. 29 2020 STAT115 Lect9.1 scRNA-seq Batch Effect Removal
  30. 30 2020 STAT115 Lect9.2 Gene Expression Module Summary
  31. 31 2020 STAT115 Lect9.3 Gene Expression Analysis Scenario
  32. 32 STAT115 Chapter 10.1 Transcription Regulation
  33. 33 STAT115 Chapter 10.2 Expectation Maximization for Motif Finding
  34. 34 STAT115 Chapter 10.3 Gibbs Sampling for Motif Finding
  35. 35 STAT115 Chapter 10.4 Motif Finding General Practices
  36. 36 STAT115 Chapter 11.1 ChIP-seq
  37. 37 STAT115 Chapter 11.2 ChIP-seq Peak Calling with MACS and QC
  38. 38 STAT115 Chapter 11.3 TF Interactions from ChIP-seq
  39. 39 STAT115 Chapter 11.4 TF Target Genes from ChIP-seq
  40. 40 2020 STAT115 Lect12.1 Epigenetics
  41. 41 2020 STAT115 Lect12.2 DNA Methylation
  42. 42 2020 STAT115 Lect12.3 DNA Methylation Function
  43. 43 2020 STAT115 Lect12.4 Nucleosome Positioning
  44. 44 2020 STAT115 Lect13.1 Histone Modifications
  45. 45 2020 STAT115 Lect13.2 Histone marks on enhancers
  46. 46 2020 STAT115 Lect13.3 Histone marks on genes
  47. 47 STAT115 Chapter 13.7 DNase-seq
  48. 48 2020 STAT115 Lect13.5 ATAC-seq
  49. 49 2020 STAT115 Lect15.1 HiC Introduction
  50. 50 2020 STAT115 Lect15.2 Topologically Associating Domains
  51. 51 2020 STAT115 Lect15.3 Chromatin Compartments
  52. 52 2020 STAT115 Lect15.4 Regulatory Network
  53. 53 2020 STAT115 Lect16.1 Intro to Single-Cell ATAC-seq
  54. 54 2020 STAT115 Lect16.2 Preprocessing and QC scATAC-seq
  55. 55 2020 STAT115 Lect16.3 Analysis of scATAC-seq
  56. 56 2020 STAT115 Lect16.4 Integrating scATAC-seq with scRNA-seq
  57. 57 2020 STAT115 Lect17.1 Module II Review
  58. 58 2020 STAT115 Lect17.2 Module II Practice Scenarios
  59. 59 Overview of Cistrome Related Tools from Liu Lab
  60. 60 2020 STAT115 Lect17.3 SNP and GWAS Intro
  61. 61 2020 STAT115 Lect17.4 GWAS Artifacts and eQTL
  62. 62 STAT115 Chapter 18.1 Intro Functional Annotate GWAS
  63. 63 STAT115 Chapter 18.2 GWAS Functional Enrichment
  64. 64 STAT115 Chapter 18.3 Find Causal SNPs
  65. 65 STAT115 Chapter 18.4 Predict disease risk
  66. 66 STAT115 GWAS Catalogue
  67. 67 STAT115 HaploReg
  68. 68 STAT115 LD Link
  69. 69 STAT115 Chapter 23.1 Introduction to Cancer Genome Analysis
  70. 70 STAT115 Chapter 23.2 Cancer. Mutation Characterization
  71. 71 STAT115 Chapter 23.3 Cancer Mutation Patterns
  72. 72 STAT115 Chapter 23.4 Tumor Purity and Clonality
  73. 73 STAT115 Chapter 23.5 Interpret Tumor Mutations
  74. 74 STAT115 Chapter 23.6 Find Cancer Genes
  75. 75 STAT115 Chapter 23.7 Summary and Future
  76. 76 STAT115 OpenCRAVAT Demo
  77. 77 STAT115 Chapter 24.1 Tumor Subtypes
  78. 78 STAT115 Chapter 24.2 Survival Analysis
  79. 79 STAT115 Chapter 24.3 Oncogenes and Tumor Suppressor Mutations
  80. 80 STAT115 Chapter 24.4 Cancer Epigenetics
  81. 81 2020 STAT115 Lect20.5 Cancer Hallmarks
  82. 82 STAT115 Chapter 26.1 Intro to Cancer Immunotherapy
  83. 83 STAT115 Chapter 26.2 HLA and Neoantigen Presentation
  84. 84 2020 STAT115 Lect22.3 Tumor Immune Deconvolution
  85. 85 2020 STAT115 Lect22.4 Immune Receptor Repertoires
  86. 86 2020 STAT115 Lect23.1 Immune Signaling
  87. 87 2020 STAT115 Lect23.2 Immunotherapy Biomarkers
  88. 88 2020 STAT115 Lect23.3 CRISPR Screens
  89. 89 2020 STAT115 Lect23.4 CRISPR Screen Computational Challenges
  90. 90 2020 STAT115 Lect24.1 Module III Review
  91. 91 2020 STAT115 Lect24.2 Course Review
  92. 92 2020 STAT115 Lect24.3 Final Logistics

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